Spiral microfluidics has been used in this study to isolate infected epithelial cells containing intracellular bacterial communities (IBCs) from other cells (RBCs, WBCs, and bacteria), in urine. Epithelial cells in human urine are 20 μm to 160 μm in size and hence traditional size based spiral microfluidic isolation cannot be used effectively. We isolated ~60% of epithelial cells by combining Dean Flow Fractionation with switched focusing mode at > 98% purity. We then use the proposed method for the isolation of epithelial cells from infected mice urine and show the presence of IBCs in the isolated cells as a proof of concept. © 2020 CBMS-0001